Article
Biochemistry & Molecular Biology
Kim C. Heimsch, Christoph G. W. Gertzen, Anna Katharina Schuh, Thomas Nietzel, Stefan Rahlfs, Jude M. Przyborski, Holger Gohlke, Markus Schwarzlaender, Katja Becker, Karin Fritz-Wolf
Summary: This study describes an improved redox biosensor, sfroGFP2, which can be used to measure oxidative effects within small cells. sfroGFP2 exhibits improved fluorescence intensity and structural stability, making it of significant interest for studying oxidative processes in small cells such as Plasmodium.
ANTIOXIDANTS & REDOX SIGNALING
(2022)
Article
Chemistry, Physical
Qi Han, Timothy M. Ryan, Carlos J. Rosado, Calum J. Drummond, Tamar L. Greaves
Summary: This study aimed to investigate the effects of ionic liquids (ILs) on the fluorescence and aggregation behavior of superfolder green fluorescent protein (sfGFP). Results showed that sfGFP was less aggregated with nitrate-based ILs compared to in buffer, but more aggregated in mesylate-based ILs. Additionally, polyol additives in IL-water mixtures slightly decreased sfGFP aggregation propensity.
JOURNAL OF COLLOID AND INTERFACE SCIENCE
(2021)
Article
Biochemistry & Molecular Biology
Peiyu Zhong, Ziying Wang, Shihao Cheng, Yiran Zhang, He Jiang, Rui Liu, Yu Ding
Summary: This study determined the crystal structure of the nanobody Nb2 complexed with superfolder GFP (sfGFP) and found that despite low sequence similarity with LaG16, they both bound to the same epitope of GFP. Nb2 showed slightly higher binding affinity for sfGFP than LaG16, and exhibited the highest melting temperature (Tm) among the tested GFP-specific nanobodies, making it a promising candidate for applications under harsh conditions. Additionally, some GFP nanobodies were shown to simultaneously bind with GFP and assemble into multifunctional complexes, providing atomic-scale binding information for further development of GFP-nanobody based fusion protein manipulation techniques.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2021)
Article
Chemistry, Multidisciplinary
Suranjan K. Paul, John M. Herbert
Summary: Liquid microjet photoelectron spectroscopy is commonly used to measure VIEs of aqueous solutes, with sensitivity to bulk versus interfacial solvation environments. Computational studies of aqueous-phase VIEs for inorganic anions show excellent agreement with experiment, regardless of simulation data restrictions. Sensitive to ion-water hydrogen bonding, short-range solvation structure is similar in both environments, making it impossible to discriminate between the two based on VIE.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Chemistry, Multidisciplinary
Boya Zhao, Lara V. V. Gillan, Andrew D. D. Scully, Anthony S. R. Chesman, Boer Tan, Xiongfeng Lin, Jingying Liu, Kevin J. J. Rietwyk, Siqi Deng, Christopher Bailey, Yi-Bing Cheng, Dane R. R. McCamey, Udo Bach
Summary: Back-contact architectures have the potential to enhance the efficiencies of perovskite solar cells (PSCs) by eliminating parasitic light absorption. However, the performance of back-contact PSCs is limited by inadequate carrier diffusion in perovskite. In this study, we demonstrate that perovskite films with a preferred out-of-plane orientation exhibit improved carrier dynamic properties. By adding guanidine thiocyanate, the films show significantly increased carrier lifetimes and mobilities, leading to enhanced carrier diffusion and improved charge collection. This approach enables the achievement of reproducible efficiencies of up to 11.2% in back-contact PSCs.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Medicine, Research & Experimental
Mehdi Roshanian Bakhsh, Leila Rouhi, Kamran Ghaedi, Mehrdad Hashemi, Maryam Peymani, Saeed Samarghandian
Summary: The aim of this study was to identify a specific gene for TNBC and target it for treatment. It was found that the expression level of KCNG1 gene was significantly higher in TNBC compared to other BC subtypes, and it was sensitive to platinum-based drugs. Moreover, Guanidine hydrochloride (GuHCl) could be used as an inhibitor to treat TNBC.
BIOMEDICINE & PHARMACOTHERAPY
(2023)
Article
Biochemistry & Molecular Biology
Qian Hou, Surajit Chatterjee, Paul E. Lund, Krishna C. Suddala, Nils G. Walter
Summary: This study investigates the thermodynamic and kinetic folding properties of two riboswitches from different bacteria and the effects of urea and trimethylamine N-oxide (TMAO) on their folding. The results show that the riboswitch from a thermophilic bacterium is more thermotolerant and that urea destabilizes their folded structure while TMAO counteracts urea denaturation. These findings shed light on how subtle sequence adaptations in a thermophilic bacterium can stabilize a common RNA structure.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Engineering, Chemical
Catherine J. Edward, Mariette Smart, Susan T. L. Harrison
Summary: Biooxidation is an established pretreatment technology used in refractory gold mineral processing. This study evaluated the impact of remediated cyanidation tailings effluent and different SCN- concentrations on a biooxidation microbial community. Results showed that remediated effluent performed similarly to defined medium in terms of microbial growth and Fe2+ oxidation activity, with only a slight delay in Fe2+ oxidation observed.
MINERALS ENGINEERING
(2022)
Article
Environmental Sciences
Li Yang, Yu-Xi Feng, Yu-Juan Lin, Xiao-Zhang Yu
Summary: The study demonstrated that treatment with sodium hydrosulfide and proline effectively repaired the chloroplast dysfunction in rice plants under SCN- stress, with different mechanisms of action. Sodium hydrosulfide stimulated processes in the PSII repair cycle, while proline mainly enhanced the expression of related genes under stress conditions.
Article
Chemistry, Multidisciplinary
Markus Joos, Maurice Conrad, Sebastian Bette, Rotraut Merkle, Robert E. Dinnebier, Thomas Schleid, Joachim Maier
Summary: Hydration of anhydrous LiSCN by water vapor leads to the formation of LiSCN•H2O, with an α-phase crystallizing at room temperature and transforming into a higher temperature β-phase at 49 degrees C. Structural and thermodynamic investigations suggest that LiSCN•H2O is a unique case compared to other LiSCN hydrates.
JOURNAL OF PHYSICS AND CHEMISTRY OF SOLIDS
(2022)
Article
Biochemistry & Molecular Biology
Jimmy Sampedro-Guerrero, Vicente Vives-Peris, Aurelio Gomez-Cadenas, Carolina Clausell-Terol
Summary: The role of salicylic acid (SA) in plant development was studied using Arabidopsis thaliana. Free SA treatment affected root and rosette growth, while encapsulated SA reduced the deleterious effects. Encapsulation allows for controlled release of SA, mitigating its damage on plant growth.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemical Research Methods
Fanfan Hao, Laxmi N. Mishra, Prasoon Jaya, Richard Jones, Jeffrey J. Hayes
Summary: Linker histones (H1s) are important for stabilizing chromatin structure and regulating transcription. The C-terminal domain (CTD) of H1 is involved in binding to chromatin and condensing upon nucleosome binding. Phosphorylation is a common modification in H1, but its specific effects and locations are unclear. Mass spectrometry techniques were used to identify phosphorylation sites in the CTD of linker histone Xenopus H1.0 and investigate its effects on chromatin structure.
MOLECULAR & CELLULAR PROTEOMICS
(2022)
Article
Environmental Sciences
Liufang Wang, Pei Luo, Chunyu Jiang, Jianlin Shen, Feng Liu, Runlin Xiao, Jinshui Wu
Summary: This study investigates the effects of biochar on soil macropore characteristics, and finds that the effects of biochar vary with the addition rate and soil depth. In the surface soil, biochar treatments increase macroporosity but decrease circularity, while in deeper soil layers the opposite effects are observed. The expansion and occupying effects of biochar also differ at different depths. Therefore, the depth-dependent macropore structure should be considered when assessing the influence of biochar on soil properties and environmental effects.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Biochemistry & Molecular Biology
Robert J. Trachman, Adrian R. Ferre-D'Amare
Summary: The ykkC-I riboswitch class shows divergent evolution, with K+ ion chelation and solvent tuning affecting ligand specificity and affinity among the riboswitches. The Burkholderia structure reveals a unique ion triad in the guanidine-binding pocket, suggesting a novel mechanism for RNA-ligand interactions. This study highlights how natural selection has shaped the versatile RNA fold of ykkC-I riboswitches.
Article
Chemistry, Inorganic & Nuclear
Alena Shlyaykher, Frank Tambornino
Summary: The crystallographic study of [NH4][SeCN] and Ag[SeCN] is presented for the first time. [NH4][SeCN] is a sensitive compound, while Ag[SeCN] is stable under various conditions. The reactivity between them resulted in the formation of [NH4][Ag(SeCN)(2)] and [NH4](3)[Ag(SeCN)(4)]. The characterization of both compounds was performed using various techniques such as single-crystal and powder X-ray diffraction, thermal analysis, and spectroscopy.
INORGANIC CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Alexander V. Fonin, Sergey A. Silonov, Anna S. Fefilova, Olesya V. Stepanenko, Anastasia A. Gavrilova, Alexey V. Petukhov, Anna E. Romanovich, Anna L. Modina, Tatiana S. Zueva, Evgeniy M. Nedelyaev, Nadejda M. Pleskach, Mirya L. Kuranova, Irina M. Kuznetsova, Vladimir N. Uversky, Konstantin K. Turoverov
Summary: The study revealed that the C-terminal domains of PML isoforms are capable of forming dynamic liquid droplet compartments, regardless of the ordered N-terminal RBCC motifs. This suggests a significant role of non-specific interactions in the liquid-liquid phase separation leading to the formation of PML bodies.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Biochemistry & Molecular Biology
Anna S. Fefilova, Alexander Fonin, Innokentii E. Vishnyakov, Irina M. Kuznetsova, Konstantin K. Turoverov
Summary: Stress is an inevitable part of life, and organisms have developed mechanisms to combat stress, including the assembly of stress-induced membraneless organelles. These organelles serve to protect the genetic and protein material of cells during stressful conditions.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Anna I. Sulatskaya, Olga V. Stepanenko, Maksim I. Sulatsky, Ekaterina V. Mikhailova, Irina M. Kuznetsova, Konstantin K. Turoverov, Olesya V. Stepanenko
Summary: This study defines the structural rearrangements of the amyloidogenic 8-barrel superfolder GFP prior to fibrillogenesis and characterizes the early intermediate nativelike state and second intermediate state. The findings provide important insights into the process of protein transformation from 8-barrel structure to amyloid fiber structure and offer clues for understanding the mechanism of protein amyloid formation.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2022)
Article
Biochemistry & Molecular Biology
Olga V. Stepanenko, Irina M. Kuznetsova, Konstantin K. Turoverov, Olesya V. Stepanenko
Summary: Understanding the photophysical properties and stability of near-infrared fluorescent proteins based on bacterial phytochromes is crucial for designing efficient fluorescent probes. It has been found that the covalent binding of the natural ligand biliverdin to these proteins leads to higher quantum yield of fluorescence and increased stability due to rigid fixation of the chromophore in the chromophore-binding pocket.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Editorial Material
Biochemistry & Molecular Biology
Irina M. Kuznetsova, Konstantin K. Turoverov
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Biochemistry & Molecular Biology
Anastasia A. Gavrilova, Anna S. Fefilova, Innokentii E. Vishnyakov, Irina M. Kuznetsova, Konstantin K. Turoverov, Vladimir N. Uversky, Alexander V. Fonin
Summary: At the beginning of the 21st century, it became clear that there were significant changes in the concept of living matter and intracellular organization. Phase transitions of biopolymers, such as intrinsically disordered proteins and RNA, play a crucial role in the spatiotemporal organization of intracellular space. Stress-induced reorganization of intracellular space forms membrane-less organelles, such as nuclear A-bodies and nuclear stress bodies, through liquid-liquid phase separation of intrinsically disordered proteins and non-coding RNA. This review focuses on the functions, structure, and formation mechanism of these membrane-less organelles.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Biochemistry & Molecular Biology
Olga Povarova, Iuliia A. Antifeeva, Alexander Fonin, Konstantin K. Turoverov, Irina M. Kuznetsova
Summary: To date, it has been shown that liquid-liquid phase separation (LLPS) plays a role in various cellular processes, providing a new perspective on the spatiotemporal organization of the cell. This new paradigm helps answer long-standing unanswered questions, particularly in the regulation of cytoskeleton assembly/disassembly and actin polymerization. Coacervates of actin-binding proteins formed during LLPS integrate with G-actin to initiate polymerization, while liquid droplet coacervates formed by signaling proteins on the inner side of the cell membrane intensify the activity of actin-binding proteins involved in actin polymerization, such as N-WASP and Arp2/3.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Konstantin G. Chernov, Kyrylo Yu. Manoilov, Olena S. Oliinyk, Daria M. Shcherbakova, Vladislav V. Verkhusha
Summary: Optogenetic systems driven by yellow-orange light are required for simultaneous regulation of multiple cellular processes. The red fluorescent protein FusionRed has been engineered into an optogenetic module called degFusionRed, which efficiently performs light-controlled transcription and targeted protein degradation. Unlike other fluorescent protein-based optogenetic domains, degFusionRed undergoes proteasomal degradation upon illumination, avoiding self-inactivation through reactive oxygen species generation. Its spectral compatibility with blue and near-infrared-light-controlled optogenetic tools and autocatalytically formed chromophore provide advantages over exogenous chromophore-dependent optogenetic tools.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Yakov I. I. Mokin, Anastasia A. A. Gavrilova, Anna S. S. Fefilova, Irina M. M. Kuznetsova, Konstantin K. K. Turoverov, Vladimir N. N. Uversky, Alexander V. V. Fonin
Summary: In this study, the formation and functioning of membrane-less organelles, A-bodies and nSBs, were investigated. It was found that these organelles have different morphology and function, as well as differences in protein composition and propensity for liquid-liquid phase separation (LLPS). Weak interactions play a crucial role in the formation and functioning of these important organelles.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Biochemistry & Molecular Biology
Sergey A. Silonov, Eugene Y. Smirnov, Irina M. Kuznetsova, Konstantin K. Turoverov, Alexander V. Fonin
Summary: In this review, the recent progress in understanding the role of individual domains of PML protein, its post-translational modifications, and polyvalent nonspecific interactions in the formation of PML bodies is highlighted. A new hypothetical model of PML body formation is proposed based on the available literature.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)